Perry's first writing work was the short story Question Mark Pyjamas in the second volume of the Virgin Decalog anthology series: this was the first story that Perry wrote with his long-term writing partner Mike Tucker. This was followed by several stories for the BBC Short Trips anthology, again all co-written with Tucker.

In October 1997, the first book in Tucker and Perry's self-styled Season 27 run was publish as part of BBC Books' Past Doctor Adventures series. The book, Illegal Alien, was rumoured to be based on a script which was in consideration for production had a twenty-seventh season of Doctor Who gone ahead. Tucker and Perry continued to write their Season 27 stories, with the novels Matrix (1998), Storm Harvest (1999), and Loving the Alien (2003).

In 2003, Tucker and Perry also wrote the novella Companion Piece for Telos Publishing Ltd.'s range of Doctor Who novellas, introducing a new companion, Catherine Broome.